Lyophilization for bacteria preservation: a promising approach for Yersinia pestis strains from an unique collection in Brazil (Fiocruz-CYP).

Yersinia pestis, the causative agent of plague, is a highly virulent bacterium that poses a significant threat to human health. Preserving this bacterium in a viable state is crucial for research and diagnostic purposes. This paper presents and evaluates a simple lyophilization protocol for the long-term storage of Y. pestis strains from Fiocruz-CYP, aiming to explore its impact on viability and long-term stability, while replacing the currently used methodologies. The lyophilization tests were conducted using the non-virulent Y. pestis strain EV76, subjected to the lyophilization process under vacuum conditions. Viability assessment was performed to evaluate the effects of lyophilization and storage conditions on Y. pestis under multiple temperature conditions (- 80 °C, - 20 °C, 4-8 °C and room temperature). The lyophilization protocol employed in this study consistently demonstrated its efficacy in maintaining high viability rates for Y. pestis samples in a up to one year follow-up. The storage temperature that consistently exhibited the highest recovery rates was - 80 °C, followed by - 20 °C and 4-8 °C. Microscopic analysis of the post-lyophilized cultures revealed preserved morphological features, consistent with viable bacteria. The high viability rates observed in the preserved samples indicate the successful preservation of Y. pestis using this protocol. Overall, the presented lyophilization protocol provides a valuable tool for the long-term storage of Y. pestis, offering stability, viability, and functionality. By refining the currently used methods of lyophilization, this protocol can improve long-term preservation for Y. pestis strains collections, facilitating research efforts, diagnostic procedures, and the development of preventive and therapeutic strategies against plague.

Genomic Analysis of Yersinia pestis Strains from Brazil: Search for Virulence Factors and Association with Epidemiological Data.

Yersinia pestis, the etiological agent of the plague, is considered a genetically homogeneous species. Brazil is currently in a period of epidemiological silence but plague antibodies are still detected in sentinel animals, suggesting disease activity in the sylvatic cycle. The present study deployed an in silico approach to analyze virulence factors among 407 Brazilian genomes of Y. pestis belonging to the Fiocruz Collection (1966-1997). The pangenome analysis associated several known virulence factors of Y. pestis in clades according to the presence or absence of genes. Four main strain clades (C, E, G, and H) exhibited the absence of various virulence genes. Notably, clade G displayed the highest number of absent genes, while clade E showed a significant absence of genes related to the T6SS secretion system and clade H predominantly demonstrated the absence of plasmid-related genes. These results suggest attenuation of virulence in these strains over time. The cgMLST analysis associated genomic and epidemiological data highlighting evolutionary patterns related to the isolation years and outbreaks of Y. pestis in Brazil. Thus, the results contribute to the understanding of the genetic diversity and virulence within Y. pestis and the potential for utilizing genomic data in epidemiological investigations.

CYP broth: a tool for Yersinia pestis isolation in ancient culture collections and field samples.

We developed a simple new selective LB-based medium, named CYP broth, suitable for recovering long-term stored Y. pestis subcultures and for isolation of Y. pestis strains from field-caught samples for the Plague surveillance. It aimed to inhibit the growth contaminating microorganisms and enrich Y. pestis growth through iron supplementation. The performance of CYP broth on microbial growth from different gram-negative and gram-positive strains from American Type Culture Collection (ATCC®) and other clinical isolates, field-caught rodent samples, and more importantly, on several vials of ancient Y. pestis subcultures was evaluated. Additionally, other pathogenic Yersinia species such as Y. pseudotuberculosis and Y. enterocolitica were also successfully isolated with CYP broth. Selectivity tests and bacterial growth performance on CYP broth (LB broth supplemented with Cefsulodine, Irgasan, Novobiocin, nystatin and ferrioxamine E) were evaluated in comparison with LB broth without additive; LB broth/CIN, LB broth/nystatin and with traditional agar media including LB agar without additive, and LB agar and Cefsulodin-Irgasan-Novobiocin Agar (CIN agar) supplemented with 50 µg/mL of nystatin. Of note, the CYP broth had a recovery twofold higher than those of the CIN supplemented media or other regular media. Additionally, selectivity tests and bacterial growth performance were also evaluated on CYP broth in the absence of ferrioxamine E. The cultures were incubated at 28 °C and visually inspected for microbiological growth analysis and O.D.625 nm measurement between 0 and 120 h. The presence and purity of Y. pestis growth were confirmed by bacteriophage and multiplex PCR tests. Altogether, CYP broth provides an enhanced growth of Y. pestis at 28 °C, while inhibiting contaminant microorganisms. The media is a simple, but powerful tool to improve the reactivation and decontamination of ancient Y. pestis culture collections and for the isolation of Y. pestis strains for the Plague surveillance from various backgrounds. KEY POINTS: • The newly described CYP broth improves the recuperation of ancient/contaminated Yersinia pestis culture collections • CYP broth was also efficient in reducing environmental contamination in field-capture samples, improving Y. pestis isolation • CYP broth can also be used for the isolation of Y. enterocolitica and Y. pseudotuberculosis.

Evaluation of a multi-species Protein A-ELISA assay for plague serologic diagnosis in humans and other mammal hosts.

BACKGROUND: The Hemagglutination assay (HA) is widely used in plague diagnosis, however, it has a subjective interpretation and demands high amounts of antigen and other immunobiological supplies. On the other hand, the conventional Anti-IgG ELISA is limited by the need of specific conjugates for multiple plague hosts, which leaves a gap for new diagnostic methods able to cover both the diagnosis of human cases and the epidemiological surveillance of multiple sentinel species. METHODS: We developed an ELISA Protein A-peroxidase method to detect anti-F1 antibodies across several species, including humans. To determine the cut-off and performance rates, HA results from 288 samples (81 rabbits, 64 humans, 66 rodents and 77 dogs) were used as reference. Next, we evaluated the agreement between Protein A-ELISA and Anti-IgG ELISA in an expanded sample set (n = 487). RESULTS: Optimal conditions were found with 250ng/well of F1 and 1:500 serum dilution. Protein A-ELISA showed high repeatability and reproducibility. We observed good correlation rates between the Protein A and IgG ELISAs optical densities and a higher positive/negative OD ratio for the Protein A-ELISA method. The overall sensitivity, specificity and area under the curve for Protein A-ELISA were 94%, 99% and 0.99, respectively. Similar results were observed for each species separately. In the analysis of the expanded sample set, there was a strong agreement between Protein A and IgG assays (kappa = 0.97). Furthermore, there was no cross-reaction with other common infectious diseases, such as dengue, Zika, Chagas disease, tuberculosis (humans) and ehrlichiosis, anaplasmosis and leishmaniasis (dogs). CONCLUSIONS: Altogether, the Protein A-ELISA showed high performance when compared both to HA and Anti-IgG ELISA, with a polyvalent single protocol that requires reduced amounts of antigen and can be employed to any plague hosts.

Performance assessment of a new indirect rapid diagnostic test for plague detection in humans and other mammalian hosts.

Plague is a flea-borne zoonosis that affects a wide range of mammals and still causes outbreaks in human populations yearly across several countries. While crucial for proper treatment, early diagnosis is still a major challenge in low- and middle-income countries due to poor access to laboratory infrastructure in rural areas. To tackle this issue, we developed and evaluated a new Fraction 1 capsular antigen (F1)-based rapid diagnostic test (RDT) as an alternative method for plague serological diagnosis and surveillance in humans and other mammals. In this study, 187 serum samples from humans, dogs, rodents and rabbits were retrospectively assessed using the plague RDT method. To calculate its performance, results were compared to those obtained by traditional hemagglutination (HA) and ELISA, which are well-established methods in the plague routine serodiagnosis. Remarkably, the results from RDT were in full agreement with those from the ELISA and HA assays, resulting in 100% (CI 95% = 95.5-100%) of sensitivity and 100% (CI 95% = 96.6-100%) of specificity. Accordingly, the Cohen's Kappa test coefficient was 1.0 (almost perfect agreement). Moreover, the RDT showed no cross-reaction when tested with sera from individuals positive to other pathogens, such as Y. pseudotuberculosis, Yersinia enterocolitica, Anaplasma platys, Ehrlichia canis and Leishmania infantum. Although preliminary, this study brings consistent proof-of-concept results with high performance of the Plague RDT when compared to HA and ELISA. Although further human and animal population-based studies will be necessary to validate these findings, the data presented here show that the plague RDT is highly sensitive and specific, polyvalent to several mammal species and simple to use in field surveillance or point-of-care situations with instant results.

Spatial and Temporal Distribution of Rodents during the Epizootic and Enzootic Periods of Plague, with a Focus on Exu, Northeastern Brazil.

The plague caused by the Yersinia pestis bacterium is primarily a flea-transmitted zoonosis of rodents that can also be conveyed to humans and other mammals. In this work, we analyzed the spatial and temporal distribution of rodent populations during epizootic and enzootic periods of the plague in the municipality of Exu, northeastern Brazil. The geospatial analyses showed that all the rodent species appeared through the whole territory of the municipality, with different occurrence hotspots for the different species. Important fluctuations in the rodent populations were observed, with a reduction in the wild rodent fauna following the end of a plague epizootic period, mostly represented by Necromys lasiurus and an increase in the commensal species Rattus rattus. A higher abundance of rats might lead to an increased exposure of human populations, favoring spillovers of plague and other rodent-borne diseases. Our analysis highlights the role of wild rodent species as amplifier hosts and of commensal rats (R. rattus) as preserver hosts in the enzootic period of a specific transmission infection area.

Spatiotemporal analysis of bubonic plague in Pernambuco, northeast of Brazil: Case study in the municipality of Exu.

Along with other countries in America, plague reached Brazil through the sea routes during the third pandemic. A brief ports phase was followed by an urban phase that took place in smaller inland cities and finally, it attained the rural area and established several foci where the ecological conditions were suitable for its continued existence. However, the geographic dispersion of plague in Brazil is still poorly studied. To better understand the disease dynamics, we accessed satellite-based data to trace the spatial occurrence and distribution of human plague cases in Pernambuco, Northeastern Brazil and using the municipality of Exu as study case area. Along with the satellite data, a historical survey using the Plague Control Program files was applied to characterize the spatial and temporal dispersion of cases in the period of 1945-1976. Kernel density estimation, spatial and temporal clusters with statistical significance and maximum entropy modeling were used for spatial data analysis, by means of the spatial analysis software packages. The use of geostatistical tools allowed evidencing the shift of the infection from the urban to the wild-sylvatic areas and the reemergence of cases after a period of quiescence, independent of the reintroduction from other plague areas.

Rodent hosts and flea vectors in Brazilian plague foci: a review.

Plague, caused by the Yersinia pestis bacterium, has several foci scattered throughout a large area from the Brazilian territory that ranges from the Northeastern State of Ceará to the Southeastern State of Minas Gerais and another separated area at the State of Rio de Janeiro. This review gathers data from plague control and surveillance programs on the occurrence and geographic distribution of rodent hosts and flea vectors in the Brazilian plague areas during the period of from 1952 to 2019. Furthermore, we discuss how the interaction between Y. pestis and some rodent host species may play a role in the disease dynamics. The absence of human cases nowadays in Brazil does not mean that it was eradicated. The dynamics of plague in Brazil and in other countries where it was introduced during the 3rd pandemic are quite alike, alternating epidemics with decades of quiescence. Hence, it remains an important epidemic disease of global concern. The existence of a large animal reservoir and competent vectors demonstrate a need for continuous surveillance to prevent new outbreaks of this disease in humans.

Peste, uma zoonose esquecida / Plague, a forgotten zoonosis

Objetivo: caracterizar aspectos epidemiológicos e clínicos fundamentais, discutir a metodologia do diagnóstico e tecer recomendações sobre as condutas perante a suspeição de casos de peste. Métodos: revisão bibliográfica e levantamento das internações e mortes por peste registradas no Sistema de Informações Hospitalares do Sistema Único de Saúde. Resultados e conclusões: a existência de diagnósticos equivocados de uma doença potencialmente fatal, além dos registros hipotéticos de internações e mortes, constitui um desafio a ser superado, pois espelha uma situação inaceitável, em que um possível e insólito diagnóstico não é investigado e acumula-se nos sistemas de informação.

Objective: to characterize ground epidemiological and clinical aspects of, discuss the methodology of diagnosis and draw recommendations about the management of suspect cases of plague. Methods: literature review and data collection of hospitalizations and deaths due to plague recorded in the Hospital Information System of the Unified Health System. Results and conclusions: the existence of mistaken diagnoses of a potentially fatal disease, as well as hypothetical records of hospitalization and deaths, is a challenge to be overcome, because it reflects an unacceptable panorama in which a possible and unusual diagnosis is not investigated and accumulates in the information systems.

High-resolution genome-wide analysis is essential for the identification of ambiguous Aeromonas strains.

Aeromonads are mainly opportunistic pathogens; however, many species are emerging as important human pathogens. Therefore, monitoring these bacteria and their accurate characterization of its species is highly important. Aeromonas Aer593 strain was recovered from a diarrhoea outbreak and did not group with any previously described Aeromonas species by housekeeping gene sequencing. To clarify the taxonomic position of Aer593, its genome was sequenced and analysed by multilocus phylogenetic analysis (MLPA), in silico DNA-DNA hybridization (isDDH), average nucleotide identity (ANI) and core genome-based phylogenetic analyzes. The MLPA with the housekeeping genes gyrB, rpoD, recA, dnaJ, gyrA and dnaX ranked the Aer593 isolate into an independent branch suggesting that it could represent a new species. However, the identity percentages of Aer593 to A. caviae strains using robust genomic analysis by isDDH and ANI were at least 81.3% and 97.8%, respectively, defining Aer593 as A. caviae. Multilocus sequence typing (MLST) presented an exact match against only a single allele (groL96) and the novel ST648 was assigned for this strain. The core genome-based phylogenetic analyses with a total of 863 orthologous genes also grouped the Aer593 isolate with A. caviae reference strains. These findings warn about the possibility of misidentification of some Aeromonas strains by MLPA and show that high-resolution genome-wide analysis is essential for the correct identification of ambiguous Aeromonas strains.

Incremento da baciloscopia no diagnóstico de tuberculose pulmonar em pessoas privadas de liberdade / Increment of the microscopy in the diagnosis of pulmonary tuberculosis in inmates

Objetivo: Avaliar um procedimento de fácil execução e baixo custo para incrementar o diagnóstico da tuberculose entre pessoas privadas de liberdade sem riscos de contaminação para profissionais de laboratório. Métodos: Amostras de escarro foram analisadas por baciloscopia após tratamento com hipoclorito de sódio e sedimentação espontânea em comparação à baciloscopia direta convencional, cultura pelo método Ogawa-Kudoh e o teste molecular rápido pelo sistema Xpert®MTB/RIF. Para as análises estatísticas foram empregados os programas Open Epi e SPSS. Resultados: De 436 amostras de escarro submetidas ao cultivo 71 foram positivas (verdadeiros positivos) e dessas 50 foram positivas pela baciloscopia direta convencional e 67 pela baciloscopia do escarro processado, o que corresponde a um incremento de 29% na positividade. Conclusão: O procedimento proposto preserva as vantagens e aumenta a sensibilidade da baciloscopia direta convencional. A implementação dessa técnica para diagnóstico entre grupos vulneráveis em locais de acesso e recursos limitados poderá aumentar a identificação de casos de tuberculose pulmonar.

Microscopic detection of Mycobacterium tuberculosis in direct or processed sputum smears.

INTRODUCTION: Microscopic identification of active pulmonary tuberculosis (PTB) from direct smears of sputum (DS) is widely used for detection, but has limited sensitivity. Here, we assessed the yield of acid-fast bacilli (AFB) detection in processed sputum smears (PSS). METHODS: Sputum samples were simultaneously analyzed by direct sputum smearing and after chemical treatment and spontaneous sedimentation. RESULTS: Of the 1,719 samples analyzed, 16.4% were positive for AFB in conventional DS and 21.4% in PSS, corresponding to a 30% increase in detection. CONCLUSIONS: Increased sensitivity from analyzing PSS and better safety protocols will contribute to improved detection and control of the disease.

Microscopic detection of Mycobacterium tuberculosis in direct or processed sputum smears

Abstract INTRODUCTION: Microscopic identification of active pulmonary tuberculosis (PTB) from direct smears of sputum (DS) is widely used for detection, but has limited sensitivity. Here, we assessed the yield of acid-fast bacilli (AFB) detection in processed sputum smears (PSS). METHODS: Sputum samples were simultaneously analyzed by direct sputum smearing and after chemical treatment and spontaneous sedimentation. RESULTS: Of the 1,719 samples analyzed, 16.4% were positive for AFB in conventional DS and 21.4% in PSS, corresponding to a 30% increase in detection. CONCLUSIONS: Increased sensitivity from analyzing PSS and better safety protocols will contribute to improved detection and control of the disease.

Seroprevalence and spatial distribution dynamics of Yersinia pestis antibodies in dogs and cats from plague foci in the State of Ceará, Northeastern Brazil

Abstract INTRODUCTION: In Brazil, the plague is established in several foci located mainly in the northeastern part of the country, where it alternates between active and quiescent periods. These foci in the State of Ceará have high epidemiological importance. In addition to other plague detection activities, plague areas can be monitored through serological surveys of dogs and cats (domestic carnivores), which, following feeding on plague-infected rodents, can develop mild to severe forms of the disease and produce long-lasting antibodies. This study aimed to characterize the circulation dynamics and spatial distribution of Yersinia pestis antibodies in dogs and cats in plague foci areas of Ceará. METHODS: An ecological study was conducted to analyze the temporal series and spatial distribution of secondary data obtained from domestic carnivore serum surveillance in Ceará's plague areas from 1990 to 2014. RESULTS: Joinpoint analysis revealed that the overall trend was a reduction in antibody-positive animals. The mean proportion of antibody-positivity during the whole study period was 1.5% (3,023/203,311) for dogs, and 0.7% (426/61,135) for cats, with more than 4% antibody-positivity in dogs in 1997 and 2002. Antibody titers ranging from 1/16 to 1/64 were frequent. Despite fluctuations and a significant reduction, in recent years, there were antibody-positive animals annually throughout the study period, and the localities containing antibody-positive animals increased in number. CONCLUSION: Yersinia pestis is actively circulating in the study areas, posing a danger to the human population.

Genetic diversity and virulence potential of clinical and environmental Aeromonas spp. isolates from a diarrhea outbreak.

BACKGROUND: Aeromonas spp. are gram-negative bacteria that can cause a variety of infections in both humans and animals and play a controversial role in diarrhea outbreaks. Our aim was to identify clinical and environmental Aeromonas isolates associated with a cholera outbreak in a northeast county of Brazil at the species level. We also aimed to determine the genetic structure of the bacterial population and the virulence potential of the Aeromonas isolates. METHODS AND RESULTS: Analysis based on concatenated sequences of the 16S rRNA and gyrB genes suggested the classification of the 119 isolates studied into the following species: A. caviae (66.9%), A. veronii (15.3%), A. aquariorum (9.3%), A. trota (3.4%), A. hydrophila (3.4%) and A. jandaei (1.7%). One isolate did not fit any Aeromonas species assessed, which might indicate a new species. The haplotype network based on 16S rRNA gene sequences identified 59 groups among the 119 isolates and 26 reference strains, and it clustered almost all A. caviae isolates into the same group. The analysis of the frequency patterns of seven virulence-associated genes (alt, ast, hlyA, aerA, exu, lip, flaA/B) revealed 29 virulence patterns composed of one to seven genes. All the isolates harbored at least one gene, and three of them harbored all seven virulence genes. CONCLUSION: The results emphasize the need to improve local water supply and maintain close monitoring of possible bacterial contamination in the drinking water.

Ehrlichia canis and Rickettsia spp. in dogs from urban areas in Paraiba state, northeastern Brazil.

The aims of our study was to identify Ehrlichia canis and antibodies against Rickettsia spp. belonging to the spotted fever group (SFG) in dogs sampled from Paraiba state, northeastern Brazil. Blood and serum samples collected by convenience from dogs in urban areas of five municipalities were analyzed by real-time PCR for the detection of E. canis DNA and by immunofluorescence assay test (IFAT) for the identification of antibodies against Rickettsia rickettsii, R. felis, R. parkeri, R. amblyommii and R. rhipicephali antigens. E. canis DNA was detected in 8.9% (64/719) of the blood samples, whereas 5.63% (43/763) of the serum samples were positive for at least one of the Rickettsia antigens tested by IFAT. This study showed for the first time the occurrence of E. canis and suggested the circulation of SFG Rickettsia in dogs in the study region of Paraiba state, northeastern Brazil.

Ehrlichia canis and Rickettsia spp. in dogs from urban areas in Paraiba state, northeastern Brazil / Ehrlichia canis e Rickettsia spp. em cães de áreas urbanas da Paraíba, nordeste do Brasil

Abstract The aims of our study was to identify Ehrlichia canis and antibodies against Rickettsia spp. belonging to the spotted fever group (SFG) in dogs sampled from Paraiba state, northeastern Brazil. Blood and serum samples collected by convenience from dogs in urban areas of five municipalities were analyzed by real-time PCR for the detection of E. canis DNA and by immunofluorescence assay test (IFAT) for the identification of antibodies against Rickettsia rickettsii, R. felis, R. parkeri, R. amblyommii and R. rhipicephali antigens. E. canis DNA was detected in 8.9% (64/719) of the blood samples, whereas 5.63% (43/763) of the serum samples were positive for at least one of the Rickettsia antigens tested by IFAT. This study showed for the first time the occurrence of E. canis and suggested the circulation of SFG Rickettsia in dogs in the study region of Paraiba state, northeastern Brazil.

Resumo Os objetivos do nosso estudo foram identificar Ehrlichia canis e anticorpos contra Rickettsia spp. pertencentes ao Grupo da Febre Maculosa (GFM) em cães amostrados no estado da Paraíba, nordeste do Brasil. As amostras de sangue e soro, coletados por conveniência, de cães em áreas urbanas de cinco municípios foram analisadas por PCR em tempo real para a detecção de DNA de E. canis e pela Reação de Imunofluorescência Indireta (RIFI) para identificação de anticorpos contra Rickettsia rickettsii, R. felis, R. parkeri, R. amblyommii e R. rhipicephali. O DNA de E. canis foi detectado em 8,9% (64/719) das amostras de sangue, enquanto que 5,63% (43/763) das amostras de soro foram positivas para pelo menos um dos antígenos de Rickettsia testados por RIFI. Este estudo mostrou pela primeira vez a ocorrência de E. canis e sugere a circulação de Rickettsia do GFM em cães na região em estudo do estado da Paraíba, Nordeste do Brasil.